Good Morning Sir/Ma'am,
The Civil Prep Program is generally offered to candidates who are qualified in every arena, but just might have a small chance of getting in that year for a variety of reasons (such as their district is very competitive), so West Point offers an Association of Graduates scholarship for the candidate to choose a military junior college for one year. I was one of these candidates last year, and I never received an actual TWE from West Point.
I think Civil Prep is a wonderful thing. I went to Marion Military Institute in Marion, Alabama last year. It was a year for me to mature, make friends, be independent, focus on my studies, and get ready for a West Point environment. I took essentially the same classes at Marion that I am currently taking as a USMA plebe, and it has helped me tremendously.
I think a lot of kids/parents are initially disappointed when they receive news of Civil Prep because this simply means another year without an appointment. However, in hindsight, I don't know a single person who regrets their year at CP.
I never think less of kids who didn't get in to West Point on the first try. I passed the CFA/APFT, had a 34/35 ACT, lots of leadership, and a decent GPA. I still think I needed prep. It made the transition a lot easier.
I am currently a plebe at USMA. Please let me know if you have any specific questions about USMA or Civil Prep. Good luck to your son!